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Y Brun

Publications and source records attributed to Y Brun.

At least 19 recordsLinked to original sources
PubMed2003

The Karyote physico-chemical genomic, proteomic, metabolic cell modeling system.

Modeling approaches to the dynamics of a living cell are presented that are strongly based on its underlying physical and chemical processes and its hierarchical spatio-temporal organization. Through the inclusion of a broad spectrum of processes and a rigorous analysis of the multiple scale nature of cellular dynamics, we are attempting to advance cell modeling and its applications. The presentation focuses on our cell modeling system, which integrates data archiving and quantitative physico-chemical modeling and information theory to provide a seamless approach to the modeling/data analysis endeavor. Thereby the rapidly growing mess of genomic, proteomic, metabolic, and cell physiological data can be automatically used to develop and calibrate a predictive cell model. The discussion focuses on the Karyote cell modeling system and an introduction to the CellX and VirusX models. The Karyote software system integrates three elements: (1) a model-building and data archiving module that allows one to define a cell type to be modeled through its reaction network, structure, and transport processes as well as to choose the surrounding medium and other parameters of the phenomenon to be modeled; (2) a genomic, proteomic, metabolic cell simulator that solves the equations of metabolic reaction, transcription/translation polymerization and the exchange of molecules between parts of the cell and with the surrounding medium; and (3) an information theory module (ITM) that automates model calibration and development, and integrates a variety of data types with the cell dynamic computations. In Karyote, reactions may be fast (equilibrated) or slow (finite rate), and the special effects of enzymes and other minority species yielding steady-state cycles of arbitrary complexities are accounted for. These features of the dynamics are handled via rigorous multiple scale analysis. A user interface allows for an automated generation and solution of the equations of multiple timescale, compartmented dynamics. Karyote is based on a fixed intracellular structure. However, cell response to changes in the host medium, damage, development or transformation to abnormality can involve dramatic changes in intracellular structure. As this changes the nature of the cellular dynamics, a new model, CellX, is being developed based on the spatial distribution of concentration and other variables. This allows CellX to capture the self-organizing character of cellular behavior. The self-assembly of organelles, viruses, and other subcellular bodies is being addressed in a second new model, VirusX, that integrates molecular mechanics and continuum theory. VirusX is designed to study the influence of a host medium on viral self-assembly, structural stability, infection of a single cell, and transmission of disease.

Animals↗
PubMed2002

Gradient separation of polymers at critical point of adsorption.

Theoretical and experimental analysis of interaction polymer chromatography revealed a new mode of polymer separation: gradient elution at the critical point of adsorption (the eluent composition where size-exclusion and adsorption interactions completely compensate each other). This mode allows for molecular-mass-independent separation by chemical composition and/or other structural differences between macromolecules. The isocratic and gradient elution of narrow polydispersity polystyrenes and poly(methylmethacrylates) on reversed- and normal-phase columns confirmed all basic theoretical assumptions and conclusions. The gradient separation of poly(alkylmethacrylate) and poly(alkylacrylate) blends, as well as styrene-butadiene copolymers provided further experimental verification of the theory.

Adsorption↗
PubMed2001

Molecular techniques open up new vistas for typing of coagulase-negative staphylococci.

Several methods were used to type 64 clinical isolates of coagulase-negative staphylococci (CNS) derived from hospitals in Morocco. The clinical isolates originated principally from blood cultures and wound sources. These isolates provided the opportunity to substantially compare the proficiency of developing molecular techniques with conventional phenotypic tests for use in the identification of clinical staphylococci. The following molecular methods were examined: Utility ribotyping analysis (Ribotyping); PCR analysis performed with 16S-23S ribosomal-DNA intergenic spacer (ITS-PCR); PCR-based random amplified polymorphic DNA (RAPD). The results obtained by the molecular techniques were contrasted to those of conventional phenotypic tests. Conventional phenotypic tests allowed the outright recognition of the majority of isolates (50/64). These 50 isolates were subdivided into 33 novobiocin-susceptible and 17 novobiocin-resistant strains of CNS. However, 2 other novobiocin-susceptible and 12 other novobiocin-resistant isolates remained unclassified by these tests. There was a good agreement between the conventional phenotypic tests and RAPD for the 33 novobiocin-susceptible isolates. But, the RAPD technique permitted the assignment of the two unidentified novobiocin-susceptible isolates to the Staphylococcus hominis species. A complete correlation was obtained between the three molecular tools for recognition of the 12 novobiocin-resistant isolates that were not identified by phenotypic typing; these were in fact identified as 5 Staphylococcus cohnii and 4 Staphylococcus equorum. Three isolates remained unidentified by all three systems of molecular techniques.

Bacterial Proteins↗
PubMed2000

Clonal dissemination of epidemic methicillin-resistant Staphylococcus aureus in Belgium and neighboring countries.

OBJECTIVES: To determine the diversity of pulsed-field gel electrophoresis (PFGE) types among epidemic strains of methicillin-resistant Staphylococcus aureus (MRSA) recovered in Belgium, France, Germany and The Netherlands over the period 1981-94. METHODS: MRSA strains collected in a multicenter survey in Belgium (n = 171) and from reference laboratories in neighboring countries (n = 102) were characterized by PFGE analysis using the SmaI enzyme. RESULTS: In total, 32 PFGE types were found. Epidemic PFGE type 1, first recognized in 1984, accounted for 82% of Belgian strains (87% of hospitals) and 51% of European MRSA strains. Four other internationally epidemic PFGE types (types 8, 10, 11 and 12) were less widely disseminated and more recently detected (1991-94), each recovered from two or three countries. International spread of two PFGE types was linked to transfer of colonized patients to Dutch hospitals from another country where this type was frequently recovered. CONCLUSIONS: Genotypic analysis indicated widespread distribution of several outbreak-associated MRSA strains over large European regions, which was in some instances related to interhospital patient transfer. These findings underscore the need for standardized international surveillance and control of MRSA transmission between healthcare institutions across Europe.

Bacteriophage Typing↗
PubMed2000

In vitro antitumor activity of 9-nitro-camptothecin as a single agent and in combination with other antitumor drugs.

Preclinical studies at Roswell Park Cancer Institute by Minderman, Cao, and Rustum (unpublished results) showed that a combination of SN-38 and 5-FU against HCT-8 human colon carcinoma cells in vitro was synergistic, with the best interaction occurring when the drugs were added sequentially, SN-38 first. Their in vivo studies using HCT-8 tumor xenografts implanted s.c. in nude athymic mice demonstrated superior efficacy for a sequential i.v. administration of CPT-11, 24 hr before 5-FU. On the basis of these studies, our group has begun to evaluate effects of RFS2000 (9-nitro-20(S)-camptothecin) (9-NC) in combination with a series of other antitumor agents. Using a panel of human tumor cell lines including A121 ovarian cancer, HCT-8 colon cancer, H-460 NSCLC, HT-1080 fibrosarcoma, and MCF7 mammary cancer, we found that a 2-hr exposure to 9-NC resulted in ID50 values of < 1.0 microM, whereas continuous exposure to drug resulted in ID50 values of < 1.0 nM. Tumor growth inhibitory activities of 5-FU, gemcitabine, and paclitaxel were determined for comparison. Combinations of these agents were evaluated with 9-NC using the human HCT-8 colon tumor cell line. Concurrent and sequential combinations of 9-NC with 5-FU had some regions of the concentration-effect surface with local synergy and some with local antagonism. However, sequential combination of 9NC or SN-38 followed by 5-FU, 24 hr later appeared to be highly synergistic at high dose-effect levels (i.e., ID90), suggesting that sequential drug administration may be more efficacious at high effect level and that the order of drug addition is very important. Overall, our results were similar to that found earlier by Rustum's group with CPT11 (or SN-38) and 5-FU, suggesting that sequential combination of 9-NC (or other camptothecin analogues) followed by 5-FU has potential for the treatment of cancer in man.

Antineoplastic Agents↗
PubMed1999

Distribution of Staphylococcus sciuri subspecies among human clinical specimens, and profile of antibiotic resistance.

The distribution of three subspecies comprising Staphylococcus sciuri was determined for a collection of 30 clinical isolates originating from Morocco, the United Kingdom, and France. The sources of these isolates were principally wounds, skin, and soft tissue infections. At the species level, the isolates were identified according to biochemical characteristics and at the subspecies level by the ribotyping technique. PCR analysis performed with the 16S-23S ribosomal DNA intergenic spacer was less powerful for subspecies differentiation. S. sciuri subsp. sciuri was the most frequent subspecies (21 isolates) found in the collection, whereas S. sciuri subsp. rodentium (seven isolates) and S. sciuri subsp. carnaticus (two isolates) were less common. mecA or a mecA-related gene was detected by PCR and Southern blot in all 30 S. sciuri isolates, supporting the suggestion that S. sciuri species are the natural reservoir of the mecA gene. While the linA/linA' gene coding for lincomycin resistance was present in five isolates, an uncharacterized gene for this resistance was suspected in seventeen other isolates.

Bacterial Typing Techniques↗
PubMed1999

Recommended minimal standards for description of new staphylococcal species. Subcommittee on the taxonomy of staphylococci and streptococci of the International Committee on Systematic Bacteriology.

In accordance with Recommendation 30b of the International Code of Nomenclature of Bacteria, minimal standards are proposed for the genus Staphylococcus and the description of newly recognized species in this genus. Assignment of a strain to the genus Staphylococcus requires that it is a Gram-positive coccus that forms clusters, produces catalase, has an appropriate cell wall structure (including peptidoglycan type and teichoic acid presence) and G + C content of DNA in a range of 30-40 mol%. The recommended minimal standards for describing a new Staphylococcus species are based on the results of phenotypic and genomic studies of at least five independently isolated strains. They include colony morphology and the results of the following conventional tests: pigment production, growth requirements, fermentative and oxidative activity on carbohydrates, novobiocin susceptibility, enzymic activities (nitrate reductase, alkaline phosphatase, arginine dihydrolase, ornithine decarboxylase, urease, cytochrome oxidase, staphylocoagulase in rabbit plasma, heat-stable nuclease, amidases, oxidases, clumping factor, and haemolytic activity on sheep or bovine blood agar). DNA-DNA hybridization experiments may distinguish species when the difference between the binding in the homologous reaction and the binding in the heterologous reaction expressed as a percentage is less than 70%. In addition, rRNA signature sequence criteria, ribotyping characterization of the nomenclature type strain and other strains of the species, and reference strains of other species is recommended to describe the strains of the new species with sets of genetic attributes and reveal possible grouping errors. This proposal has been endorsed by the members of the Subcommittee on the taxonomy of staphylococci and streptococci of the international Committee on Systematic Bacteriology.

Animals↗
PubMed1998

Experimental study of antidiarrheal activity of Salicairine.

Experimental antidiarrheal activity of a traditionally used medication, Salicairine, was demonstrated in comparison to loperamide by significant inhibition of castor oil-induced diarrhea in mice (increases in hard faeces/total faeces ratio of 38 and 54 and 5 and 54% with respect to controls, at 0.5 and 1 mL/kg and 1 and 2 mg/kg, respectively) and bisacodyl-induced increase in large intestine transit in rats (125 and 280 and 210% with respect to controls, at 0.4 and 2 mL/kg Salicairine and 5 mg/kg loperamide, respectively). Salicairine was able to reduce contractions of isolated rat duodenum induced by barium chloride and acetylcholine, although not completely (that is about 60%) as seen with loperamide. Also, it did not change normal gastrointestinal transit in mice at doses of 0.5 to 1 mL/kg, conversely to loperamide which had a significant effect (decrease of 50%) at 2 mg/kg. Finally, Salicairine at 0.01 mL/mL, like loperamide at 0.2 mg/mL, significantly increased net fluid absorption in rat colon, either in basal conditions (30 and 64% respectively) or after a prostaglandin E1-induced increase in net fluid secretion (41 and 35%, respectively). The antidiarrheal activity of Salicairine is possibly related, at least in part, to an increase in colon net fluid absorption or a decrease in net fluid secretion.

Acetylcholine↗
PubMed1997

Identification of atypical strains of Staphylococcus epidermidis by use of molecular tools.

Four atypical coagulase-negative staphylococcal (CNS) isolates from clinical sources were compared with Staphylococcus epidermidis strains by ribotyping. The ribotypes of the four strains shared close rDNA restriction profiles with those of the S. epidermidis strains used. The DNA sequence encoding 16S rRNA demonstrated 99.9% homology with S. epidermidis. S1 nuclease experiments showed that these atypical strains formed a homogeneous genomic group. DNA-DNA homologies between the S. epidermidis type strain CCM 2124 and the four CNS isolates ranged from 70 to 89%. The guanine-plus-cytosine content of the deoxyribonucleic acid of the four strains ranged from 31 to 32 mol%.

Amino Acids↗
PubMed1997

Comparative performances of six agglutination kits assessed by using typical and atypical strains of Staphylococcus aureus.

Six commercial agglutination tests designed for the identification of Staphylococcus aureus were compared by using a strain collection which included 512 staphylococci representing 33 species (318 isolates of Staphylococcus aureus [including 144 oxacillin resistant], 46 S. epidermidis isolates, 15 S. haemolyticus isolates, 12 S. saprophyticus isolates, 29 S. schleiferi isolates, 30 S. lugdunensis isolates, and 62 other coagulase-negative staphylococci). This group also included a proportion of strains with unusual phenotypes (e.g., 19 coagulase-negative S. aureus isolates, 26 clumping factor-negative S. aureus isolates, and 4 S. aureus isolates each with a double deficiency). The overall sensitivity for identification of typical and atypical S. aureus was high with the Staphaurex Plus test (Murex Biotech) (99.7%), the Pastorex Staph Plus test (Sanofi Diagnostics Pasteur) (99.7%), and the Slidex Staph Plus test (bioMérieux) (100%). The overall rate of specificity was affected by the unusual inclusion in this study of a high proportion of non-S. aureus species, such as S. lugdunensis and S. schleiferi, which express a clumping factor and therefore produce a positive result with the agglutination tests.

Agglutination Tests↗
PubMed1996

Enterotoxin production by coagulase-negative staphylococci isolated from goats' milk and cheese.

An antigen related to the Enterotoxin E from Staphylococcus aureus was produced by ten of 187 coagulase-negative staphylococci (CNS) isolated from goats' milk, whey and cheese in quantities ranging from 10 to 90 ng/ml supernatant. The enterotoxin-producing strains were identified at the species level as S. simulans, S. xylosus, S. equorum, S. lentus and S. capitis. Detection of the enterotoxins was done by the VIDAS SET test (bioMérieux) and by an indirect double-sandwich ELISA technique using anti-enterotoxin monoclonal antibodies. The results obtained were further confirmed by Southern blotting, using two radioactive oligonucleotide probes that hybridized specifically with the gene of S. aureus coding for the enterotoxin E.

Animals↗
PubMed1996

Identification of micrococcaceae isolated from goat's milk and cheese in the Poitou-Charentes region.

One hundred and ninety strains of coagulase-negative staphylococci were isolated from goat's milk, whey and cheese at various stages of manufacture. Sixteen different coagulase negative Staphylococci (CNS) species were recovered, 3 of which were predominant: Staphylococcus simulans, Staphylococcus epidermidis and Staphylococcus xylosus. The prevalent species were recovered at least at two different stages of cheese manufacturing, suggesting a better adaptation to the environment. After 15 days of ripening, the cheeses showed lower counts of Micrococcaceae.

Animals↗
PubMed1996

Identification and ribotyping of Staphylococcus xylosus and Staphylococcus equorum strains isolated from goat milk and cheese.

Twenty-five strains of staphylococci isolated from goat milk and cheese were identified as belonging to the Staphylococcus xylosus/equorum group using the ID 32 Staph system (bioMérieux, Marcy-L'Etoile, France). This system, however, was not able to discriminate between these two species for 19 of the strains tested. Ribotyping was performed on these 25 strains, as well as on three reference strains of each of these two species. Hybridization membranes were scanned and analyzed using the Taxotron software package (Taxolab, Institut Pasteur, Paris, France). A dendrogram representation showed that ribotypes were distributed in two clear-cut clusters corresponding to S. equorum (21 strains) and S. xylosus (four strains).

Animals↗
PubMed1996

Phenotypic and genotypic (pulsed-field gel electrophoresis) characteristics of enterotoxin-A-producing Staphylococcus aureus strains.

The phenotypic (antibiotype, serotype, phagetype) and genotypic (SmaI restriction patterns using pulsed-field gel electrophoresis) characters of 162 Staphylococcus aureus epidemiologically unrelated strains were studied. Eighty-two of the isolates produced enterotoxin-A (SEA+), while 80 produced none (SEA-). None of the phenotypic characters observed were characteristic of SEA+ strains. On the other hand, the electrophoretic profiles revealed a non-random distribution of the SEA+ strains (p < 0.01 in groups PI and PIII, and p < 0.03 in group PII). It can therefore reasonably be assumed that the enterotoxin-A-producing strains did not constitute a single clone, but rather, seemed to belong to strains derived from at least three clones with distinct genetic organization.

DNA, Bacterial↗
PubMed1996

Staphylococcus saprophyticus subsp. bovis subsp. nov., isolated from bovine nostrils.

A new coagulase-negative subspecies, Staphylococcus saprophyticus subsp. bovis, is described on the basis of a study of five strains isolated from the anterior nares of cows. This subspecies is differentiated from the other novobiocin-resistant staphylococci by its phenotypic properties, cell wall composition, and levels of genetic relatedness. The type strain of the new subspecies is KV 12 (=CCM 4410).

Animals↗
PubMed1994

[Antibiotic prophylaxis in heart surgery].

Cardiac surgery enters mainly into the class I of Altemeier ("clean surgery"). However, many factors may explain an intraoperative contamination: surgery of long duration, extra-corporeal circulation, aspiration of blood and air, immunodepression...). In fact, the infectious risk decreases from about 25% with placebo to 5% with prophylactic antibiotics. The staphylococcal infections are the most frequent (mediastinitis, endocarditis, parietal infections...). Cephalosporins, particularly of second-generation type (cefamandole, cefuroxime), perform better than antistaphylococcal penicillins. The combination with an amino-side may be used when Gram negative bacilli infection prevalence is high. Vancomycin is efficient but hypotension and renal impairment have been reported. Therefore, vancomycin is used in patients allergic to cephalosporins, when a high prevalence of methicillin-resistant Staphylococcus or enterococci infections is reported, or when the patient has recently received broad-spectrum antimicrobial therapy. The antibiotic doses must take into account the haemodilution due to extracorporeal circulation and the necessity to obtain sufficient serum concentrations throughout surgery. A prophylaxis of more than 48 hours is not associated with an improved outcome. In cardiac transplantation a prophylaxis is essential, but is still questioned during the insertion of pace-markers. In any case, the antibiotic prophylaxis must take into account the bacterial prevalence of each institution.

Aminoglycosides↗
PubMed1994

Clotting activity in Staphylococcus schleiferi subspecies from human patients.

Staphylococcus schleiferi subsp. schleiferi is a coagulase-negative staphylococcus, usually present as a contaminant in human specimens. A near relative, S. schleiferi subsp. coagulans, possesses coagulase activity but has not been reported from humans. We here describe three isolates of pseudocoagulase-positive S. schleiferi subsp. schleiferi and one isolate of S. schleiferi subsp. coagulans from human patients. The pseudocoagulase from the S. schleiferi subsp. schleiferi isolates differs from S. aureus staphylocoagulase by being sensitive to a combination of protease inhibitors (aprotinin, N-ethylmaleimide, and heparin). These isolates could all easily be confused with S. aureus in a typical clinical laboratory, since they all possess a heat-stable DNase and promote clotting formation. Moreover, S. schleiferi subsp. coagulans produces protein A, and S. schleiferi subsp. schleiferi expresses a clumping factor (fibrinogen affinity factor). Southern blot hybridization with an S. aureus coa-specific probe revealed no sequence related to the coa gene in any of the S. schleiferi isolates, and their riboprobe profiles and biochemical characteristics were typical of S. schleiferi subspecies, not of S. aureus. This study demonstrates that both subspecies of S. schleiferi can promote clotting of rabbit plasma in the standard tube test for coagulase.

Animals↗